Structural stability of the solvated cellulose IIII crystal models: A molecular dynamics study

Cellulose

Volumn 16, Issue 2, 2009, Pages 151-165

  Yui, Toshofumi ^a   Hayashi, Sachio ^a  

^a UNIVERSITY OF MIYAZAKI   (Japan)

Author keywords

Cellulose IIII; Crystal modeling; Molecular dynamics; Structure conversion

Indexed keywords

CELLULOSE; DYNAMICS; MOLECULAR DYNAMICS; STABILITY;

BASE PLANES; CHAIN ARRANGEMENTS; CRYSTAL MODELS; IMPLICIT SOLVENTS; LATTICE PLANES; LOCAL TRANSFORMATIONS; MD SIMULATIONS; MOLECULAR-DYNAMICS SIMULATIONS; PERIODIC BOUNDARIES; SOLVENT EFFECTS; STRUCTURAL STABILITIES; STRUCTURE CONVERSION; VACUUM SYSTEMS;

CRYSTAL STRUCTURE;

CELLULOSE; CONVERSION; CRYSTAL STRUCTURE; DYNAMICS; MOLECULAR WEIGHT; SOLVENTS; STABILITY; WATER;

CELLULOSE; COMPUTER SIMULATION; CRYSTALLINITY; MOLECULAR STRUCTURE; OLIGOMER;

EID: 60549101508     PISSN: 09690239     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10570-008-9265-x     Document Type: Article

References (55)

1. Aabloo S, French AD (1994) Preliminary potential energy calculations of cellulose Iα crystal structure. Macromol Theor Simul 3:185-191. doi: 10.1002/mats.1994.040030115
2. Allinger NL, Yuh YH, Lii JH (1989) Molecular mechanics. The MM3 force field for hydrocarbons. 2. Vibrational frequencies and thermodynamics. J Am Chem Soc 111:8551-8566. doi: 10.1021/ja00205a001
3. Allinger NL, Raman M, Lii JH (1990) A molecular mechanics force field (MM3) for alcohols and ethers. J Am Chem Soc 112:8293-8307. doi: 10.1021/ ja00179a012
4. Attala R, VanderHart DL (1984) Native cellulose: A composite of two distinct crystalline forms. Science 223:283-285. doi: 10.1126/ science.223.4633.283
5. Basma M, Sundara S, Calgan D, Venali T, Woods RJ (2001) Solvated ensemble averaging in the calculation of partial atomic charges. J Comput Chem 22:1125-1137. doi: 10.1002/jcc.1072
6. Bergenstråhle M, Berglund LA, Mazequ K (2007) Thermal response in crystalline Iβ cellulose: A molecular dynamics study. J Phys Chem B 111:9138-9145. doi: 10.1021/jp072258i
7. Brooks BR, Bruccoleri RE, Olafson BD, Swaminathan S, Karplus M (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187-217. doi: 10.1002/jcc.540040211
8. Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Wang B, Pearlman DA, Crowley M, Brozell S, Tsui V, Gohlke H, Mongan J, Homak V, Cui G, Beroza P, Schafmeister C, Caldwell JW, Ross WS, Kollman P (2004) AMBER 8. University of California, San Francisco
9. 13C-NMR and electron microscopy study on the reversible cellulose I → cellulose III I transformation in Valonia. Carbohydr Res 160:1-11. doi: 10.1016/0008-6215(87)80299-9
10. Essmann U, Pereta L, Berkowitz ML, Darden TA, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577-8593. doi: 10.1063/1.470117
11. Ford ZM, Stevens ED, Johnson GP, French AD (2005) Determining the crystal structure of cellulose III I by modeling. Carbohydr Res 340:827-833. doi: 10.1016/j.carres.2005.01.028
12. French AD, Dowd MK (1993) Exploration of disaccharide conformations by molecular mechanics. J Mol Struct THEOCHEM 286:183-201. doi: 10.1016/ 0166-1280(93)87162-7
13. French AD, Miller DP (1993) Comparisons of hydrogen bonding in small carbohydrate molecules by diffraction and MM3(92) calculations. In: Smith DA (ed) Modeling the hydrogen bond. ACS symp ser, 569. American Chemical Society, Washington DC, pp 235-251
14. French AD, Miller DP, Aabloo S (1993) Miniature crystal models of cellulose polymorphs and other carbohydrates. Int J Biol Macromol 15:30-36. doi: 10.1016/S0141-8130(05)80085-6
15. Hardy BJ, Sarko A (1996) Molecular dynamics simulations and diffraction-based analysis of the native cellulose fibre: Structural modelling of the I-α and I-β phases and their interconversion. Polymer 37:1833-1839. doi: 10.1016/0032-3861(96)87299-5
16. Hawkins GD, Cramer CJ, Truhlar DG (1995) Pairwise solute descreening of solute charges from a dielectric medium. Chem Phys Lett 246:122-129. doi: 10.1016/0009-2614(95)01082-K
17. Hawkins GD, Cramer CJ, Truhlar DG (1996) Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J Phys Chem 100:19824-19839. doi: 10.1021/jp961710n
18. Hiener AP, Telman O (1997) Interface between monoclinic crystalline cellulose and water: Breakdown of the odd/even duplicity. Langmuir 13:511-518. doi: 10.1021/la960886d
19. Heiner AP, Kuutti L, Telman O (1998) Comparison of the interface between water and four surfaces of native crystalline cellulose by molecular dynamics simulations. Carbohydr Res 306:205-220. doi: 10.1016/ S0008-6215(97)10053-2
20. Humphrey W, Dalke A, Schulten K (1996) VMD: Visual molecular dynamics. J Mol Graph 14:33-38. doi: 10.1016/0263-7855(96)00018-5
21. Jorgensen WL, Chandrasekhar J, Madura J, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926-935. doi: 10.1063/1.445869
22. Kirchner KN, Woods RJ (2001a) Solvent interactions determine carbohydrate conformation. Proc Natl Acad Sci USA 98:10541-10545. doi: 10.1073/pnas.191362798
23. Kirchner KN, Woods RJ (2001b) Quantum mechanical study of the nonbonded forces in water-methanol complexes. J Phys Chem A 105:4150-4155. doi: 10.1021/jp004413y
24. Kolpak FJ, Blackwell J (1975) The structure of regenerated cellulose. Macromolecules 8:563-564. doi: 10.1021/ma60046a037
25. Kroon-Batenburg LMJ, Bouma B, Kroon J (1996) Stability of cellulose structures studied by MD simulations. Could mercerized cellulose II be parallel? Macromolecules 29:5695-5699. doi: 10.1021/ma9518058
26. Kuttel M, Brady JW, Naidoo KJ (2002) Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. J Comput Chem 23:1236-1243. doi: 10.1002/jcc.10119
27. Langan P, Nishiyama Y, Chanzy H (2001) X-ray structure of mercerized cellulose II at 1 Å resolution. Biomacromolecules 2:410-416. doi: 10.1021/bm005612q
28. Langan P, Sukumar N, Nishiyama Y, Chanzy H (2005) Synchrotron X-ray structures of cellulose Iβ and regenerated cellulose II at ambient temperature and 100 K. Cellulose 12:551-562. doi: 10.1007/ s10570-005-9006-3
29. Mann J, Marrinan HJ (1958) Crystalline modifications of cellulose: Part II. A study with plane-polarized infrared radiation. J Polym Sci 32:357-370. doi: 10.1002/pol.1958.1203212507
30. Marrinan HJ, Mann J (1956) Infrared spectra of the crystalline modification of cellulose. J Polym Sci 21:301-311. doi: 10.1002/ pol.1956.120219812
31. Matthews JF, Skopec C, Mason PE, Zuccato P, Torget RW, Sugiyama J, Himmel ME, Brady JW (2006) Computer simulation studies of microcrystalline cellulose Iβ. Carbohydr Res 341:138-152. doi: 10.1016/j.carres.2005.09.028
32. Mazeau K, Heux L (2003) Molecular dynamics simulations of bulk native crystalline and amorphous structures of cellulose. J Phys Chem B 107:2394-2403. doi: 10.1021/jp0219395
33. Mazeau K, Vergelati C (2002) Atomistic modeling of the adsorption of benzophenone onto cellulosic surfaces. Langmuir 18:1919-1927. doi: 10.1021/la010792q
34. Nishiyama Y, Langan P, Chanzy H (2002) Crystal structure and hydrogen-bonding system in cellulose Iβ from synchrotron X-ray and neutron fiber diffraction. J Am Chem Soc 124:9074-9082. doi: 10.1021/ ja0257319
35. Nishiyama Y, Sugiyama J, Chanzy H, Langan P (2003) Crystal structure and hydrogen bonding system in cellulose Iα from synchrotron X-ray and neutron fiber diffraction. J Am Chem Soc 125:14300-14306. doi: 10.1021/ ja037055w
36. Nyertz S, Pizzi A, Merlin A, Maigret B, Brown D, Deglise X (2000) A new all-atom force field for crystalline cellulose I. J Appl Polym Sci 78:1939-1946. doi:10.1002/ 1097-4628(20001209)78:11<1939::AID-APP130>3.0.CO;2-9
37. Palma R, Zuccato P, Himmel ME, Liang G, Brady JW (2001) Molecular mechanics studies of cellulases. In: Himmel ME, Baker JO, Saddler JN (eds) Glycosyl hydrolases in biomass conversion. ACS symp ser. American Chemical Society, Washington DC, pp 112-130
38. Rao VSR, Qasba PK, Balaji PV, Chandrasekaran R (1998) Fiber diffraction analysis of polysaccharides. In: Conformation of carbohydrates. Harwood Academic Publishers, Amsterdam, pp 223-254, and references therein
39. Roche E, Chanzy H (1981) Electron microscopy study of the transformation of cellulose I into cellulose III I in Valonia. Int J Biol Macromol 3:201-206. doi: 10.1016/0141-8130(81)90064-7
40. Ryckaert JP, Cicotti G, Berendsen HJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:327-341. doi: 10.1016/ 0021-9991(77)90098-5
41. Sarko A (1978) What is the crystalline structure of cellulose? Tappi 61:59-61
42. Sarko A, Southwick J, Hayashi J (1976) Packing analysis of carbohydrates and polysaccharides. 7. Crystal structure of cellulose III I and its relationship to other cellulose polymorphs. Macromolecules 9:857-863. doi: 10.1021/ma60053a028
43. Stipanovic AJ, Sarko A (1976) Packing analysis of carbohydrates and polysaccharides. 6. Molecular and crystal structure of regenerated cellulose II. Macromolecules 9:851-857. doi: 10.1021/ma60053a027
44. Sugiyama J, Vuong R, Chanzy H (1991) Electron diffraction study of the two crystalline phases occurring in native cellulose from an algal cell wall. Macromolecules 24:4168-4175. doi: 10.1021/ma00014a033
45. Tanaka F, Fukui N (2004) The behavior of cellulose molecules in aqueous environment. Cellulose 11:33-38. doi: 10.1023/B:CELL.0000014769.01795.7f
46. Tanaka F, Okamura K (2005) Characterization of cellulose molecules in bio-system studied by modeling methods. Cellulose 12:243-252. doi: 10.1007/s10570-004-5864-3
47. VanderHart DL, Attala R (1984) Studies of microstructure in native celluloses using solid-state carbon-13 NMR. Macromolecules 17:1465-1472. doi: 10.1021/ma00138a009
48. I to Iβ. Macromolecules 34:3271-3275. doi: 10.1021/ma0013354
49. I prepared in supercritical ammonia. Macromolecules 34:1237-1243. doi: 10.1021/ ma001406z
50. I crystal structure and hydrogen bonding by synchrotron X-ray and neutron fiber diffraction. Macromolecules 37:8548-8555. doi: 10.1021/ma0485585
51. Weiser J, Shenkin PS, Still WC (1999) Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comput Chem 20:217-230. doi:10.1002/ (SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A
52. I. Biomacromolecules 8:817-824. doi: 10.1021/bm060867a
53. Yui T, Ogawa K (2005) X-ray diffraction study of polysaccharides. In: Dumitriu S (ed) Polysaccharides, structural diversity and functional versatility, 2nd edn. Marcel Dekker, New York, pp 99-122, and reference therein
54. Yui T, Nishimura S, Akiba S, Hayashi S (2006) Swelling behavior of the cellulose Iβ crystal models by molecular dynamics. Carbohydr Res 341:2521-2530. doi: 10.1016/j.carres.2006.04.051
55. Yui T, Taki N, Sugiyama J, Hayashi S (2007) Exhaustive crystal structure search and crystal modeling of β-chitin. Int J Biol Macromol 40:336-344. doi: 10.1016/j.ijbiomac.2006.08.017